Description Usage Arguments Details Author(s) Examples
Keep a fraction of the links (gene pairs) with the higher correlation values than user given threshold (specified with 'cutoff').
1 2 | rLinkfilter(exprs.1, exprs.2, cutoff = 0.8,
r.method = c("pearson", "spearman")[1])
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exprs.1 |
a data frame or matrix for condition A, with rows as variables (genes) and columns as samples. |
exprs.2 |
a data frame or matrix for condition B, with rows as variables (genes) and columns as samples. |
cutoff |
the threshold of correlation coefficient value. Default is 0.8. |
r.method |
a character string to indicate which type of correlation coefficient, 'pearson' (default) or 'spearman', will be computed. |
Each gene link is associated with two correlation values (one out of condition A and the other out of condition B) and thus a list of 'maximum absolute values' of the two values is decided. Then these links have larger correlation coefficient than threshold are kept.
Bao-Hong Liu, Hui Yu, Jing Yang
1 2 | data(exprs)
rLinkfilter(exprs[1:100,1:16],exprs[1:100,17:63],cutoff=0.8,r.method='pearson')
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